The study of the recognition or lack of recognition of cancer cells by a host organism has proceeded in many different directions. Understanding of the field presumes some understanding of both basic immunology and oncology.
Early research on mouse tumors revealed that these displayed molecules which led to rejection of tumor cells when transplanted into syngeneic animals. These molecules are “recognized” by T cells in the recipient animal, and provoke a cytolytic T cell response with lysis of the transplanted cells. This evidence was first obtained with tumors induced in vitro by chemical carcinogens, such as methylcholanthrene. The antigens expressed by the tumors and which elicited the T cell response were found to be different for each tumor. See Prehn, et al., J. Natl. Canc. Inst., 18: 769-778 (1957); Klein, et al., Cancer Res., 20:1561-1572 (1960); Gross, Cancer Res., 3:326-333 (1943), Basombrio, Cancer Res., 30:2458-2462 (1970) for general teachings on inducing tumors with chemical carcinogens and differences in cell surface antigens. This class of antigens has come to be known as “tumor specific transplantation antigens” or “TSTAs”. Following the observation of the presentation of such antigens when induced by chemical carcinogens, similar results were obtained when tumors were induced in vitro via ultraviolet radiation. See Kripke, J. Natl. Canc. Inst., 53:333-1336 (1974).
While T cell mediated immune responses were observed for the types of tumor described supra, spontaneous tumors were thought to be generally non-immunogenic. These were therefore believed not to present antigens which provoked a response to the tumor carrying subject. See Hewitt, et al., Brit. J. Cancer, 33:241-259 (1976).
The family of tum− antigen presenting cell lines are immunogenic variants obtained by mutagenesis of mouse tumor cells or cell lines, as described by Boon, et al., J. Exp. Med., 152:1184-1193 (1980), the disclosure of which is incorporated by reference. To elaborate, tum− antigens are obtained by mutating tumor cells which do not generate an immune response in syngeneic mice and will form tumors (i.e., “tum+” cells). When these tum+ cells are mutagenized, they are rejected by syngeneic mice, and fail to form tumors (thus “tum−”). See, Boon, et al., Proc. Natl. Acad. Sci USA, 74:272 (1977), the disclosure of which is incorporated by reference. Many tumor types have been shown to exhibit this phenomenon. See, e.g., Frost, et al., Cancer Res., 43:125 (1983).
It appears that tum− variants fail to form progressive tumors because they elicit an immune rejection process. The evidence in favor of this hypothesis includes the ability of “tum−” variants of tumors, i.e., those which do not normally form tumors, to do so in mice with immune systems suppressed by sublethal irradiation, Van Pel, et al. Proc. Natl, Acad. Sci. USA, 76:5282-5285 (1979); and the observation that intraperitoneally injected tum− cells of mastocytoma P815 multiply exponentially for 12-15 days, and then are eliminated in only a few days in the midst of an influx of lymphocytes and macrophages (Uyttenhove, et al., J. Exp. Med., 152:1175-1183 (1980)). Further evidence includes the observation that mice acquire an immune memory which permits them to resist subsequent challenge to the same tum− variant, even when immunosuppressive amounts of radiation are administered with the following challenge to the same tum− variant, even when immunosuppressive amounts of radiation are administered with the following challenge of cells (Boon, et al., Proc. Natl, Acad. Sci. USA, 74:272-275 (1977); Van Pel, et al., supra; Uyttenhove, et al., supra). Later research found that when spontaneous tumors were subjected to mutagenesis, immunogenic variants were produced which did generate a response. Indeed, these variants were able to elicit an immune protective response against the original tumor. See Van Pel, et al., J. Exp. Med., 157:1992-2001 (1983). Thus, it has been shown that it is possible to elicit presentation of a so-called “tumor rejection antigen” in a tumor which is a target for a syngeneic rejection response. Similar results have been obtained when foreign genes have been transfected into spontaneous tumors. See Fearon, et al., Cancer Res., 48:2975-1980 (1988) in this regard.
A class of antigens has been recognized which are presented on the surface of tumor cells and are recognized by cytotoxic T cells, leading to lysis. This class of antigens will be referred to as “tumor rejection antigens” or “TRAs” hereafter. TRAs may or may not elicit antibody responses. The extent to which these antigens have been studied, has been via cytolytic T cell characterization studies, in vitro, i.e., the study of the identification of the antigen by a particular cytolytic T cell (“CTL” hereafter) subset. The subset proliferates upon recognition of the presented tumor rejection antigen, and the cells presenting the antigen are lysed. Characterization studies have identified CTL clones which specifically lyse cells expressing the antigens. Examples of this work may be found in Levy et al., Adv. Cancer Res., 24:1-59 (1977); Boon, et al., J. Exp. Med., 152:1184-1193 (1980); Brunner, et al., J. Immunol., 124:1627-1634 (1980); Maryanski, et al., Eur. J. Immunol., 124:1627-1634 (1980); Maryanski, et al., Eur. J. Immunol., 12:406-412 (1982); Palladino, et al., Canc. Res., 47:5074-5079 (1987). This type of analysis is required for other types of antigens recognized by CTLs, including minor histocompatibility antigens, the male specific H-Y antigens, and a class of antigens, referred to as “tum−” antigens, and discussed herein.
A tumor exemplary of the subject matter described supra is known as P815. See DePlaen, et al., Proc. Natl. Acad. Sci. USA, 85:2274-2278 (1988); Sikora, et al., EMBO J., 9:1041-1050 (1990), and Sibille, et al., J. Exp. Med., 172:35-45 (1990), the disclosures of which are incorporated by reference. The P815 tumor is a mastocytoma, induced in a DBA/2 mouse with methylcholanthrene and cultured as both an in vitro tumor and a cell line. The P815 line has generated many tum− variants following mutagenesis, including variants referred to as P91A (DePlaen, supra), 35B (Szikora, supra) and P198 (Sibille, supra). In contrast to tumor rejection antigens—and this is a key distinction—the tum− antigens are only present after the tumor cells are mutagenized. Tumor rejection antigens are present on cells of a given tumor without mutagenesis. Hence, with reference to the literature, a cell line can be tum+, such as the line referred to as “P1”, and can be provoked to produce tum− variants. Since the tum− phenotype differs from that of the parent cell line, one expects a difference in the DNA of tum− cell lines as compared to their tum+ parental lines, and this difference can be exploited to locate the gene of interest in tum− cells. As a result, it was found that genes of tum− variants such as P91A, 35B and P198 differ from their normal alleles by point mutations in the coding regions of the gene. See Szikora and Siblle, supra, and Lurquin, et al., Cell, 58:293-303 (1989). This has proved not to be the case with the TRAs of this invention. These papers also demonstrated that peptides derived from the tum− antigen are presented by the Ld molecule for recognition by CTLs. P91A is presented by Ld, P35 by Dd and P198 by Kd.
U.S. Pat. No. 5,342,774, the disclosure of which is incorporated by reference, disclosed three members of a family of the genes referred to hereafter as the “MAGE” family of genes. MAGEA1, A2 and A3 are disclosed therein. Also see Traversari, et al., J. Exp. Med., 176:1453-1457 (1993); van der Bruggen, et al., Science, 254:1643-147 (1991), the disclosures of which are incorporated by reference. Additional members of the MAGE family have been discovered and are disclosed in, e.g., DePlaen, et al., Immunogenetics, 40:360 (1994), and U.S. Pat. No. 5,612,201 to DePlaen, both of which are incorporated by reference. With respect to MAGEA1, in addition to the '774 patent, see e.g. U.S. Pat. No. 5,925,729.
The genes are useful as a source for the isolated and purified tumor rejection antigen precursor and the TRA themselves, either of which can be used as an agent for treating the cancer for which the antigen is a “marker”, as well as in various diagnostic and surveillance approaches to oncology, discussed infra. It is known, for example that tum− cells can be used to generate CTLs which lyse cells presenting different tum− antigens as well as tum+ cells. See, e.g., Maryanski, et al., Eur. J. Immunol., 12:401 (1982); and Van den Eynde, et al., Modem Trends in Leukemia IX (June 1990), the disclosures of which are incorporated by reference. The tumor rejection antigen precursor may be expressed in cells transfected by the gene, and then used to generate an immune response against a tumor of interest.
In the parallel case of human neoplasms, it has been observed that autologous mixed lymphocyte-tumor cell cultures (“MLTC” hereafter) frequently generate responder lymphocytes which lyse autologous tumor cells and do not lyse natural killer targets, autologous EBV-transformed B cells, or autologous fibroblasts (see Anichini, et al., Immuno. Today, 8:385-389 (1987)). This response has been particularly well studied for melanomas, and MLTC have been carried out either with peripheral blood cells or with tumor infiltrating lymphocytes. Examples of the literature in this area including Knuth, et al., Proc. Natl. Acad. Sci. USA, 86:2804-2802 (1984); Mukherji, et al., J. Exp. Med., 158:240 (1983); Hérin, et al., Int. J. Canc., 39:390-396 (1987); Topalian, et al., J. Clin. Oncol., 6:839-853 (1988). Stable cytotoxic T cell clones (“CTLs” hereafter) have been derived from MLTC responder cells, and these clones are specific for the tumor cells. See Mukherji, et al., supra, Hérin, et al., supra, Knuth, et al., supra. The antigens recognized on tumor cells by these autologous CTLs do not represent a cultural artifact, since they are found on fresh tumor cells. Topalian, et al., supra; Degiovanni, et al., Eur. J. Immul., 20:1865-1868 (1990). These observations, coupled with the techniques used herein to isolate the genes for specific murine tumor rejection antigen precursors, have led to the isolation of nucleic acid sequences coding for tumor rejection antigen precursors of TRAs presented on human tumors. It is now possible to isolate the nucleic acid sequences which code for tumor rejection antigen precursors, including, but not being limited to those most characteristic of a particular tumor, with ramifications that are described infra.
Additional work has focused upon the presentation of TRAs by the class of molecules known as human leukocyte antigens, or “HLAs”. This work has resulted in several unexpected discoveries regarding the field. Specifically, in U.S. Pat. No. 5,405,940, the disclosure of which is incorporated by reference, nonapeptides including a MAGEA3 derived peptide, are taught which are presented by HLA-A1 molecules. The reference teaches that given the known specificity of particular peptides for particular HLA molecules, one should expect a particular peptide to bind one HLA molecule, but not others. This is important, because different individuals possess different HLA phenotypes. As a result, while identification of a particular peptide as being a partner for a specific HLA molecule has diagnostic and therapeutic ramifications, these are only relevant for individuals with that particular HLA phenotype. There is a need for further work in the area, because cellular abnormalities are not restricted to one particular HLA phenotype, and targeted therapy requires some knowledge of the phenotype of the abnormal cells at issue.
Additional peptides have been identified which consist of amino acid sequences found in MAGE-3, but which bind to different MHC molecules. See, e.g., U.S. Pat. Nos. 5,554,506, 5,585,461, 5,591,430 and 6,091,987 which describe peptides which bind to HLA-A2 molecules, and also see U.S. Pat. Nos. 5,965,535, 6,291,430 and 6,369,211, which teach peptides consisting of amino acid sequences found in MAGE-3, which bind to MHC Class II molecules. See, e.g., Tanzarella, et al., Canc. Res., 59:2668-74 (1999), teaching a MAGEA3 based peptide which binds to HLA-B37, as well as Kawashima, et al., Hum Immunol., 59:1-14 (1998); Tanako, et al., Cancer Res., 57:4465-68 (1997); Oiso, et al., Int. J. Cancer, 81:387-94 (1999), and Herman, et al., Immunogenetics, 43:377-83 (1996), which collectively teach MAGEA3 based peptides which bind to HLA-A*0201, A24, B*4402 and B*4403. These papers are all incorporated by reference in their entirety.
It is important to note that different approaches have been taken to identifying the peptides described herein with different ramifications. For example, Gaugler et al., J. Exp. Med. 179:921-930 (1994) and Tanzarella, et al., supra, secured CTLs from melanoma patients following autologous, mixed lymphocyte tumor cell cultures. With respect to the other references cited herein, “motif analysis”, using information found in, e.g., Ramensee, et al., Immunogenetics, 41:178-228 (1995), incorporated by reference, was applied to the complete sequence of MAGEA3 protein to identify potential HLA molecule binders. These were then tested, and active molecules identified thereby.
This approach, i.e., employing motif analysis, has been found to exhibit a major drawback in that several peptide specific CTL generated using the synthetic peptides, do not recognize HLA matched tumor cells which express MAGE-3 endogenously. There have been two explanations proposed for this. One is that the peptides at issue are not generated efficiently by the natural processing and presentation machinery of the cells. The second is that the CTLs obtained using high concentrations of the synthetic peptides have low affinity for the target. See Dahl, et al., J. Immunol., 157:239-246 (1996).
MAGEA3 is expressed in about 75% of metastatic melanomas, and in 35-50% of esophageal, head and neck, lung. and bladder carcinomas. See, e.g., Gaugler, et al., supra. Boon, et al., Cancer Vaccines: Cancer Antigens, Shared Tumor Specific Antigens” in Rosenberg, ed., Principles and Practice of The Biologic Therapy of Cancer (Philadelphia, JB Lippincott Williams & Wilkins, 2000), pp. 493-504. Hence, there is interest in having additional methodologies available for identifying peptides consisting of sequences found in MAGEA3, especially those which form complexes with MHC molecules other than those set forth, supra.
A new strategy has been developed for identifying only naturally or well processed tumor antigens. Dendritic cells transduced with gene MAGEA3 are used as stimulator cells for autologous CD8+ T cells. See, e.g., Luiten, et al., Tissue Antigens, 55:149-152 (2000); Chaux, et al., J. Immunol., 163:2928-36 (1999); Luiten, et al., Tissue Antigens, 56:77-81 (2000); Schultz, et al., Tissue Antigens, 57:103-9 (2001), and Van den Eynde: Cancer Immunity 2001: www.cancerimmunity.org/peptidedatabase/tcellepitopes.htm., all of which are incorporated by reference, for examples of the application of this technique, with identification of relevant antigenic peptides.